6.2.1 Stability Improvements for Timing Jobs

Changes:
-Fixed handling of compressed files with the Pipeline class: changes in ra_post().
-Fixed storing of files uploaded in the Pipeline class: changes in ra_post().
-Fixes timing of multiple files: caches job timings as they are checked.
-Timings for Pipeline ids now return the file they are associated with.
-Store/Retrieve the index ('cache') of spfyids:genomehashes in MongoDB
-Store/Retrieve the largest spfyid in MongoDB

Notes:
-Should solve ~90% of the problems we were having with Blazegraph (#187)
-Will still have delays with retrieval for tasks like phylotyper or group comparisons